Beveling 4 edges of a cube to make a nut/bolt head
There are two things that can be happening:


The object has probably been scaled in object mode, but the transformation was not applied (CtrlA in object Mode).

When the transformations are not applied, the scale for transformations in edit mode can get completely out of whack. 

Read this related posts:

Why do the measurements of this object seem erroneous?

Why is it important to apply transformation to an objects data?
(probably because of the reasons above) You are using a large bevel value, the transformations are being multiplied by the scale of your object giving you a value that is much larger than the object itself, creating errors.




The fix is applying your scale in object mode, or using Percent as the amount type for the bevel making the transformations, that will allow you to have more control and prevent you  from beveling past 100%.



(But even if you do that. Start getting into the habit of applying transformations in object mode.)